State of the art high-resolution mass spectrometry allows the identification and quantification of metabolites, proteins and their post-translational modifications. In order to meet the growing MS demands of the members of the CellNetworks cluster concerning specification, resolution and throughput, two core facilities for protein mass spectrometry have been set up at the Heidelberg University Biochemistry Center (BZH) and the Zentrum für Molekulare Biologie Heidelberg (ZMBH). Mass spectrometry for analyses of metabolites is being established at the Centre for Organismal Studies Heidelberg (COS).